diff --git a/lib/WorkflowMethylseq.groovy b/lib/WorkflowMethylseq.groovy index fcd45850..6a1ac39f 100755 --- a/lib/WorkflowMethylseq.groovy +++ b/lib/WorkflowMethylseq.groovy @@ -55,12 +55,16 @@ class WorkflowMethylseq { public static String toolCitationText(params) { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report + // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", def citation_text = [ "Tools used in the workflow included:", "FastQC (Andrews 2010),", + "Trim Galore! (Krueger)", + "Bismark (Krueger 2011)", + "bwa-meth (Pedersen 2014)", + "Picard (Broad Institute 2019)", + "Qualimap (Okonechnikov 2015)", + "Preseq (Daley 2013)", "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -96,7 +100,7 @@ class WorkflowMethylseq { meta["tool_bibliography"] = "" // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") //meta["tool_bibliography"] = toolBibliographyText(params)